Support empty samples ./.

Question

pjotrp opened this issue 10 years ago · comments

bio-vcf --filter "rec.sample.clone3.ad[1]>1 and rec.sample.subclone33.dp>1" <
bioruby-vcf/test/data/input/multisample.vcf

1 10665 . C G 56.61 . AC=2;AF=0.250;AN=8; GT:AD:DP:GQ:PL ./. ./. 0/1:4,3:7:57:57,0,78 0/1:3,2:5:23:30,0,23 ./. 0/0:2,0:2:3:0,3,26 0/0:6,1:7:6:0,6,49

/Library/Ruby/Gems/2.0.0/gems/bio-vcf-0.0.2/bin/bio-vcf:115:in `eval':
undefined method '>' for nil:NilClass (NoMethodError)

Pjotr Prins · Answer 1 · Tue Mar 25 2014 02:14:30 GMT+0800 (China Standard Time)

Suggest

bio-vcf --filter "rec.sample.clone3? and rec.sample.subclone33? and rec.sample.clone3.ad[1]>1 and rec.sample.subclone33.dp>1"

or

bio-vcf --continue --filter "rec.sample.clone3.ad[1]>1 and rec.sample.subclone33.dp>1"

Pjotr Prins · Answer 2 · Thu Mar 27 2014 14:24:08 GMT+0800 (China Standard Time)

Fixed. See README and features.